Author

David Barnett

Published

June 6, 2024

Code
# load packages, do you need data packages?
library(tidyverse) # do you really need the whole tidyverse?
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.5.1     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.1
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Code
library(here)
here() starts at /Users/david/Documents/git/R-templates/html-reporto
Code
library(phyloseq)
library(microViz)
microViz version 0.12.2 - Copyright (C) 2021-2024 David Barnett
! Website: https://david-barnett.github.io/microViz
✔ Useful?  For citation details, run: `citation("microViz")`
✖ Silence? `suppressPackageStartupMessages(library(microViz))`

1 Intro

aims and preamble

2 Get data

3 Formatting examples

Code
plot(mtcars)

Code
plot(chickwts)

Code
# hello

4 Quarto Info

5 Session info

sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24)
 os       macOS Sonoma 14.5
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Amsterdam
 date     2024-06-06
 pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package          * version  date (UTC) lib source
 ade4               1.7-22   2023-02-06 [1] CRAN (R 4.4.0)
 ape                5.8      2024-04-11 [1] CRAN (R 4.4.0)
 Biobase            2.64.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 BiocGenerics       0.50.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 biomformat         1.32.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 Biostrings         2.72.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 cli                3.6.2    2023-12-11 [1] CRAN (R 4.4.0)
 cluster            2.1.6    2023-12-01 [1] CRAN (R 4.4.0)
 codetools          0.2-20   2024-03-31 [1] CRAN (R 4.4.0)
 colorspace         2.1-0    2023-01-23 [1] CRAN (R 4.4.0)
 crayon             1.5.2    2022-09-29 [1] CRAN (R 4.4.0)
 data.table         1.15.4   2024-03-30 [1] CRAN (R 4.4.0)
 digest             0.6.35   2024-03-11 [1] CRAN (R 4.4.0)
 dplyr            * 1.1.4    2023-11-17 [1] CRAN (R 4.4.0)
 evaluate           0.23     2023-11-01 [1] CRAN (R 4.4.0)
 fansi              1.0.6    2023-12-08 [1] CRAN (R 4.4.0)
 fastmap            1.2.0    2024-05-15 [1] CRAN (R 4.4.0)
 forcats          * 1.0.0    2023-01-29 [1] CRAN (R 4.4.0)
 foreach            1.5.2    2022-02-02 [1] CRAN (R 4.4.0)
 generics           0.1.3    2022-07-05 [1] CRAN (R 4.4.0)
 GenomeInfoDb       1.40.1   2024-05-24 [1] Bioconductor 3.19 (R 4.4.0)
 GenomeInfoDbData   1.2.12   2024-05-26 [1] Bioconductor
 ggplot2          * 3.5.1    2024-04-23 [1] CRAN (R 4.4.0)
 glue               1.7.0    2024-01-09 [1] CRAN (R 4.4.0)
 gtable             0.3.5    2024-04-22 [1] CRAN (R 4.4.0)
 here             * 1.0.1    2020-12-13 [1] CRAN (R 4.4.0)
 hms                1.1.3    2023-03-21 [1] CRAN (R 4.4.0)
 htmltools          0.5.8.1  2024-04-04 [1] CRAN (R 4.4.0)
 htmlwidgets        1.6.4    2023-12-06 [1] CRAN (R 4.4.0)
 httr               1.4.7    2023-08-15 [1] CRAN (R 4.4.0)
 igraph             2.0.3    2024-03-13 [1] CRAN (R 4.4.0)
 IRanges            2.38.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 iterators          1.0.14   2022-02-05 [1] CRAN (R 4.4.0)
 jsonlite           1.8.8    2023-12-04 [1] CRAN (R 4.4.0)
 knitr              1.46     2024-04-06 [1] CRAN (R 4.4.0)
 lattice            0.22-6   2024-03-20 [1] CRAN (R 4.4.0)
 lifecycle          1.0.4    2023-11-07 [1] CRAN (R 4.4.0)
 lubridate        * 1.9.3    2023-09-27 [1] CRAN (R 4.4.0)
 magrittr           2.0.3    2022-03-30 [1] CRAN (R 4.4.0)
 MASS               7.3-60.2 2024-04-24 [1] local
 Matrix             1.7-0    2024-03-22 [1] CRAN (R 4.4.0)
 mgcv               1.9-1    2023-12-21 [1] CRAN (R 4.4.0)
 microViz         * 0.12.2   2024-06-05 [1] local
 multtest           2.60.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 munsell            0.5.1    2024-04-01 [1] CRAN (R 4.4.0)
 nlme               3.1-164  2023-11-27 [1] CRAN (R 4.4.0)
 permute            0.9-7    2022-01-27 [1] CRAN (R 4.4.0)
 phyloseq         * 1.48.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 pillar             1.9.0    2023-03-22 [1] CRAN (R 4.4.0)
 pkgconfig          2.0.3    2019-09-22 [1] CRAN (R 4.4.0)
 plyr               1.8.9    2023-10-02 [1] CRAN (R 4.4.0)
 purrr            * 1.0.2    2023-08-10 [1] CRAN (R 4.4.0)
 R6                 2.5.1    2021-08-19 [1] CRAN (R 4.4.0)
 Rcpp               1.0.12   2024-01-09 [1] CRAN (R 4.4.0)
 readr            * 2.1.5    2024-01-10 [1] CRAN (R 4.4.0)
 reshape2           1.4.4    2020-04-09 [1] CRAN (R 4.4.0)
 rhdf5              2.48.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 rhdf5filters       1.16.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 Rhdf5lib           1.26.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 rlang              1.1.3    2024-01-10 [1] CRAN (R 4.4.0)
 rmarkdown          2.27     2024-05-17 [1] CRAN (R 4.4.0)
 rprojroot          2.0.4    2023-11-05 [1] CRAN (R 4.4.0)
 rstudioapi         0.16.0   2024-03-24 [1] CRAN (R 4.4.0)
 S4Vectors          0.42.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 scales             1.3.0    2023-11-28 [1] CRAN (R 4.4.0)
 sessioninfo        1.2.2    2021-12-06 [1] CRAN (R 4.4.0)
 stringi            1.8.4    2024-05-06 [1] CRAN (R 4.4.0)
 stringr          * 1.5.1    2023-11-14 [1] CRAN (R 4.4.0)
 survival           3.5-8    2024-02-14 [1] CRAN (R 4.4.0)
 tibble           * 3.2.1    2023-03-20 [1] CRAN (R 4.4.0)
 tidyr            * 1.3.1    2024-01-24 [1] CRAN (R 4.4.0)
 tidyselect         1.2.1    2024-03-11 [1] CRAN (R 4.4.0)
 tidyverse        * 2.0.0    2023-02-22 [1] CRAN (R 4.4.0)
 timechange         0.3.0    2024-01-18 [1] CRAN (R 4.4.0)
 tzdb               0.4.0    2023-05-12 [1] CRAN (R 4.4.0)
 UCSC.utils         1.0.0    2024-05-06 [1] Bioconductor 3.19 (R 4.4.0)
 utf8               1.2.4    2023-10-22 [1] CRAN (R 4.4.0)
 vctrs              0.6.5    2023-12-01 [1] CRAN (R 4.4.0)
 vegan              2.6-6.1  2024-05-21 [1] CRAN (R 4.4.0)
 withr              3.0.0    2024-01-16 [1] CRAN (R 4.4.0)
 xfun               0.44     2024-05-15 [1] CRAN (R 4.4.0)
 XVector            0.44.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 yaml               2.3.8    2023-12-11 [1] CRAN (R 4.4.0)
 zlibbioc           1.50.0   2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)

 [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library

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